Visualisation problems

Visualisation development in SSM is limited to the generation of script with in-line data for Rasmol. Answers for all Rasmol-related questions should be looked for on its web site. Installing Rasmol as a plug-in (or "helper" application) in your browser is a browser-related issue, and we probably cannot say more than we do in our recommendations posted in the SSM's Start Page. Other issues are listed below.

  1. SSM says there are no matches while I know for sure they should be there.
  2. SSM says my protein has no secondary structure, while Rasmol shows a beautiful picture of it.
  3. SSE assignments in SSM are different of what I got from somewhere else.
  4. SSM seems to lose certain SSEs
  5. SSM reports certain SSEs as unmatched in the "SSE alignment" table, however I see that they are mapped onto each other in the "3D structural alignment" table just below
  6. None from th above.

SSM says there are no matches while I know for sure they should be there.
Yes, theoretically it is possible to find a structural neighbour for any polypeptide. The only question is how remote that neighbour would be. When searching in PDB or SCOP archive, SSM does not pretend to find a PDB or SCOP structure closest to your input. The task is slightly different: to find all structures showing a certain measure of similarity to the input. This means that "less similar" structural neighbours (which make perhaps 90% of the PDB for a typical query) are not taken into account. The only reason for taking this approach is to save your time: searching through the whole PDB is expensive.

Everything is however under your control, because SSM allows you to specify the desired level of similarity. In the Submission Form, you are asked to specify the "Lowest acceptible match" for the query and target structures. By default, the similarity levels are set at 70%. This means that SSM will consider only matches where at least 70% of secondary structure elements (SSEs) of the query may be mapped, or superposed in 3D, on at least 70% of target's SSEs. By bringing these figures down you can expand the set of structures to be searched. If both levels are set to zero, the whole PDB is searched through, and then a match should be there.

SSM says my protein has no secondary structure, while Rasmol shows a beautiful picture of it.
Don't be fooled by Rasmol. It first reads annotation records in PDB files (HELIX/SHEET), and shows what they say. Remove these records in your file and load it into Rasmol again. If secondary structure has not changed, then check for another, quite frequent, reason: corrupted (read this link!) PDB file.

If you find that your PDB file complies with the standard, try to think of what else could hinder the secondary structure identification. E.g., there was a case when a user submitted an artificial structure consisting of two chains superposed on each other. Because of this superposition, the hydrogen bonding got completely screwed up and SSEs could not be identified. Intriguingly, in that case SSEs could be found for each chain separately, but not for the whole protein. That caused quite a difference in results when the same structure was submitted as two files, each containing a single chain.

If you cannot find a reason why SSM keeps saying that there is no secondary structure motifs in your protein, please tell us about that.

SSE assignments in SSM are different of what I got from somewhere else.
This is natural if the differences are small, not more than 1, maximum 2, residues on both ends of an SSE. Algorithms for secondary structure calculations have a few empirical parameters, and may give different priorities to geometrical aspects of the structure and its hydrogen bonding. SSM tends to report longer (by 1-3 residues) SSEs than DSSP. Sometimes two helices or to strands may merge, as compared to another SS-calculating algorithm, or, in opposite, an SSE may appear split in two parts.

If you find that SSE indentification is significantly different of your expectations, please check first whether your PDB file is corrupted. If you are certain that SSM is in fault, please let us know that.

SSM seems to lose certain SSEs.
This may be due to the general reasons listed right above. On top of that, SSM ignores strands shorter than 4 residues and helices shorter than 6 residues, because it was found that too short secondary structure elements tend to manifest themselves less regularly within structural families. If this does not explain your observations, please let us know.

SSMreports certain SSEs as unmatched in the "SSE alignment" table, however I see that they are mapped onto each other in the "3D structural alignment" table just below.
This is normal. SSM compares structures in two steps. In the first step it matches the protein's secondary structures, and the results are used as an intial guess for the second step, that is a precise alignment of Ca's in 3D. The "SSE alignment" table presents the results of 1st step. Certain SSEs may not match because of considerable differences in their positions and orientations relatively to other, already matched, SSEs. If such SSEs are found on a considerable distance from each other at best superposition of the structures, their Ca's do not get mapped. However, SSEs are also considered as non-matching if they significantly differ in number of residues. Thus, SSM does not match a strand of 5 residues to a strand of 10 residues even if they overlap well at best structure superposition (which indicates a difference in the hydrogen bondong patterns). However, Ca-alignment would map individual Ca's of such SSEs.

Although the above may sound somewhat confusing, but we decided to leave the things as is for having an extra indication of structural dissimilarity. The "SSE alignment" table may show in a grasp that there are considerable differences in the SSE topology and/or composition, while the "3D structural alignment" table delivers further details, allowing for figuring out how actually significant the differences are.

None from the above is my problem.
Ok, please help us and we'll do our best to help you: report your problem.